[feat] Match fauna strain names

nextstrain · Jul 3, 2023 · 125ba00 · 125ba00
1 parent 8b28622
commit 125ba00
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Showing 2 changed files with 33 additions and 4 deletions.
diff --git a/ingest/bin/post_process_metadata.py b/ingest/bin/post_process_metadata.py
@@ -35,19 +35,19 @@ def _set_strain_name(record, fixes):
     strain_name = record["strain"]
 
     if strain_name in fixes:
-        strain_name = fixes[strain_name]
+        return(fixes[strain_name])
 
     strain_name = strain_name.replace('Zika_virus', '').replace('Zikavirus', '').replace('Zika virus', '').replace('Zika', '').replace('ZIKV', '')
-    strain_name = strain_name.replace('Human', '').replace('human', '').replace('H.sapiens_wt', '').replace('H.sapiens_tc', '').replace('Hsapiens_tc', '').replace('H.sapiens-tc', '').replace('Homo_sapiens', '').replace('Homo sapiens', '').replace('Hsapiens', '').replace('H.sapiens', '')
+    strain_name = strain_name.replace('Human', '').replace('human', '').replace('H.sapiens_wt', '').replace('H.sapiens-wt', '').replace('H.sapiens_tc', '').replace('Hsapiens_tc', '').replace('H.sapiens-tc', '').replace('Homo_sapiens', '').replace('Homo sapiens', '').replace('Hsapiens', '').replace('H.sapiens', '')
     strain_name = strain_name.replace('/Hu/', '')
     strain_name = strain_name.replace('_Asian', '').replace('_Asia', '').replace('_asian', '').replace('_asia', '')
-    strain_name = strain_name.replace('_URI', '').replace('_SER', '').replace('_PLA', '').replace('_MOS', '').replace('_SAL', '')
+    strain_name = strain_name.replace('_URI', '').replace('-URI', '').replace('_SER', '').replace('-SER', '').replace('_PLA', '').replace('-PLA', '').replace('_MOS', '').replace('_SAL', '')
     strain_name = strain_name.replace('Aaegypti_wt', 'Aedes_aegypti').replace('Aedessp', 'Aedes_sp')
     strain_name = strain_name.replace(' ', '').replace('\'', '').replace('(', '').replace(')', '').replace('//', '/').replace('__', '_').replace('.', '').replace(',', '')
     strain_name = re.sub('^[\/\_\-]', '', strain_name)
 
     if strain_name in fixes:
-        strain_name = fixes[strain_name]
+        return(fixes[strain_name])
 
     try:
         strain_name = 'V' + str(int(strain_name))

diff --git a/ingest/source-data/annotations.tsv b/ingest/source-data/annotations.tsv
@@ -1,3 +1,32 @@
+KY014295	strain	USA/2016/FL010
+MT377503	strain	V151144
+MF988734	strain	SG_EHI_/33164Y17
+KU853013	strain	Dominican_Republic/2016/PD2
+KY785443	strain	USA/2016/FL028
+KX906952	strain	2016_HND_19563
+KY120348	strain	MEX_CIENI551
+KX856011	strain	Aedes_sp/MEX_I_44/2016
+KY785421	strain	USA/2016/FL019
+KU527068	strain	Natal_RGN
+MF438286	strain	Cuba_2017
+KF993678	strain	THA/PLCal_ZV/2013
+KY631494	strain	ENCB165P4
+KY785440	strain	USA/2016/FL035
+KY785451	strain	Martinique/2016/FL001
+MF664436	strain	Dominican_Republic/2016/ZB
+KY648934	strain	Aedes_aegypti/MEX/MEX_I_44/2016
+KX879603	strain	EC/Esmeraldas/062/2016
+OL414716	strain	Faranah/18
+MN185326	strain	French_Guiana_Aedes_aegypti_T1010
+MN185328	strain	French_Guiana_Aedes_aegypti_T1141
+KX827268	strain	USA/UT_1/2016
+KU853012	strain	Dominican_Republic/2016/PD1
+MK028857	strain	Puerto_Rico/2015/PRVABC59
+KY785457	strain	USA/2016/FL029
+MH513600	strain	BR/Sinop/H366_2P/2015
+KY927808	strain	ZZ_1
+KX087102	strain	COL/FLR/2015
+KX879604	strain	EC/Esmeraldas/089/2016
 AF380138	country	Democratic Republic of the Congo
 AY741551	country	Sierra Leone
 DQ011153	country	USA